59,709 research outputs found
A General Concept for Consistent Documentation of Computational Analyses
The ever-growing amount of data in the field of life sciences demands standardized ways of high-throughput computational analysis. This standardization requires a thorough documentation of each step in the computational analysis to enable researchers to understand and reproduce the results. However, due to the heterogeneity in software setups and the high rate of change during tool development, reproducibility is hard to achieve. One reason is that there is no common agreement in the research community on how to document computational studies. In many cases, simple flat files or other unstructured text documents are provided by researchers as documentation, which are often missing software dependencies, versions and sufficient documentation to understand the workflow and parameter settings. As a solution we suggest a simple and modest approach for documenting and verifying computational analysis pipelines. We propose a two-part scheme that defines a computational analysis using a Process and an Analysis metadata document, which jointly describe all necessary details to reproduce the results. In this design we separate the metadata specifying the process from the metadata describing an actual analysis run, thereby reducing the effort of manual documentation to an absolute minimum. Our approach is independent of a specific software environment, results in human readable XML documents that can easily be shared with other researchers and allows an automated validation to ensure consistency of the metadata. Because our approach has been designed with little to no assumptions concerning the workflow of an analysis, we expect it to be applicable in a wide range of computational research fields. Database URL: http://deep.mpi-inf.mpg.de/DAC/cmds/pub/pyvalid.zi
Reproducible Econometric Research. A Critical Review of the State of the Art.
Recent software developments are reviewed from the vantage point of reproducible econometric research. We argue that the emergence of new tools, particularly in the open-source community, have greatly eased the burden of documenting and archiving both empirical and simulation work in econometrics. Some of these tools are highlighted in the discussion of three small replication exercises.Series: Research Report Series / Department of Statistics and Mathematic
Skills and Knowledge for Data-Intensive Environmental Research.
The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap
Restructuring the rotor analysis program C-60
The continuing evolution of the rotary wing industry demands increasing analytical capabilities. To keep up with this demand, software must be structured to accommodate change. The approach discussed for meeting this demand is to restructure an existing analysis. The motivational factors, basic principles, application techniques, and practical lessons from experience with this restructuring effort are reviewed
Model Cards for Model Reporting
Trained machine learning models are increasingly used to perform high-impact
tasks in areas such as law enforcement, medicine, education, and employment. In
order to clarify the intended use cases of machine learning models and minimize
their usage in contexts for which they are not well suited, we recommend that
released models be accompanied by documentation detailing their performance
characteristics. In this paper, we propose a framework that we call model
cards, to encourage such transparent model reporting. Model cards are short
documents accompanying trained machine learning models that provide benchmarked
evaluation in a variety of conditions, such as across different cultural,
demographic, or phenotypic groups (e.g., race, geographic location, sex,
Fitzpatrick skin type) and intersectional groups (e.g., age and race, or sex
and Fitzpatrick skin type) that are relevant to the intended application
domains. Model cards also disclose the context in which models are intended to
be used, details of the performance evaluation procedures, and other relevant
information. While we focus primarily on human-centered machine learning models
in the application fields of computer vision and natural language processing,
this framework can be used to document any trained machine learning model. To
solidify the concept, we provide cards for two supervised models: One trained
to detect smiling faces in images, and one trained to detect toxic comments in
text. We propose model cards as a step towards the responsible democratization
of machine learning and related AI technology, increasing transparency into how
well AI technology works. We hope this work encourages those releasing trained
machine learning models to accompany model releases with similar detailed
evaluation numbers and other relevant documentation
Computational phylogenetics and the classification of South American languages
In recent years, South Americanist linguists have embraced computational phylogenetic methods to resolve the numerous outstanding questions about the genealogi- cal relationships among the languages of the continent. We provide a critical review of the methods and language classification results that have accumulated thus far, emphasizing the superiority of character-based methods over distance-based ones and the importance of develop- ing adequate comparative datasets for producing well- resolved classifications
High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)
Computing plays an essential role in all aspects of high energy physics. As
computational technology evolves rapidly in new directions, and data throughput
and volume continue to follow a steep trend-line, it is important for the HEP
community to develop an effective response to a series of expected challenges.
In order to help shape the desired response, the HEP Forum for Computational
Excellence (HEP-FCE) initiated a roadmap planning activity with two key
overlapping drivers -- 1) software effectiveness, and 2) infrastructure and
expertise advancement. The HEP-FCE formed three working groups, 1) Applications
Software, 2) Software Libraries and Tools, and 3) Systems (including systems
software), to provide an overview of the current status of HEP computing and to
present findings and opportunities for the desired HEP computational roadmap.
The final versions of the reports are combined in this document, and are
presented along with introductory material.Comment: 72 page
- âŠ